Previously on this topic: On the Care and Feeding of Young Rationalists, On Juvenile Fiction, Study: Encouraging Obedience Considered Harmful.

From what I've read, it seems like the most important thing is making rationalist thought something the child genuinely enjoys. Giving them various rationalist exercises to do, for instance, is not very useful if they're not sufficiently motivated to continue with them by the time they're no longer living with you.

You could also try to instill a habit. The following is an anecdote from a self-help book so the source isn't the most reliable in the world, but it sounds plausible:

One of the things that is great about Leo is his continued persistence in asking himself a question that his father instilled in him when from the time he was a little boy. Each day at the dinner table, his father would ask, "Leo, what have you learned today?" Leo had to have an answer, and a quality one. If he hadn't learned something really interesting in school that day, he would run and get the encyclopedia to study something that he could share. He says that to this day he won't go to bed until he's learned something new that's of value. As a result he's constantly stimulating his mind, and a great deal of his passion and love for learning has come from this question, asked repeatedly, begun decades ago.